I managed to get it to work, though, and I'd like to share it so that you can either

profit from it or

warn me if I'm doing something that is terribly wrong.

The trick is to

first compile 3.3.1 as before with the old version of winvnc.exe intact. This causes ultravnc.ini to be configured correctly. Ignore the resulting InstantSupport.exe, we will create another one shortly.

Replace winvnc.exe in SRC\InstantSupport_Files with the version you want included (I used 1.2.0.3).

Repackage everything by creating a subfolder Compiled (parallel to SRC) and executing the following in a command line in the directory directly above SRC: